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- PDB-3v4y: Crystal Structure of the first Nuclear PP1 holoenzyme -

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Basic information

Entry
Database: PDB / ID: 3v4y
TitleCrystal Structure of the first Nuclear PP1 holoenzyme
Components
  • Nuclear inhibitor of protein phosphatase 1
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsHYDROLASE / PP1 / Ser/Thr phosphatase / NIPP1 / IDP
Function / homology
Function and homology information


ribonuclease E activity / regulation of glycogen catabolic process / protein serine/threonine phosphatase inhibitor activity / negative regulation of protein dephosphorylation / PTW/PP1 phosphatase complex / glycogen granule / regulation of glycogen biosynthetic process / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases ...ribonuclease E activity / regulation of glycogen catabolic process / protein serine/threonine phosphatase inhibitor activity / negative regulation of protein dephosphorylation / PTW/PP1 phosphatase complex / glycogen granule / regulation of glycogen biosynthetic process / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / RNA catabolic process / regulation of canonical Wnt signaling pathway / regulation of translational initiation / myosin phosphatase activity / branching morphogenesis of an epithelial tube / protein serine/threonine phosphatase activity / glycogen metabolic process / protein-serine/threonine phosphatase / Triglyceride catabolism / entrainment of circadian clock by photoperiod / phosphatase activity / phosphoprotein phosphatase activity / DARPP-32 events / ribonucleoprotein complex binding / dephosphorylation / protein dephosphorylation / Downregulation of TGF-beta receptor signaling / RNA splicing / response to lead ion / adherens junction / spliceosomal complex / circadian regulation of gene expression / lung development / regulation of circadian rhythm / mRNA processing / Circadian Clock / presynapse / perikaryon / endonuclease activity / cell population proliferation / dendritic spine / nuclear speck / cell cycle / cell division / mRNA binding / glutamatergic synapse / nucleolus / DNA binding / RNA binding / extracellular exosome / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1290 / Serine-threonine protein phosphatase, N-terminal / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1290 / Serine-threonine protein phosphatase, N-terminal / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / SMAD/FHA domain superfamily / Metallo-dependent phosphatase-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / Nuclear inhibitor of protein phosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.098 Å
AuthorsPage, R. / Peti, W. / O'Connell, N.E. / Nichols, S.
CitationJournal: Structure / Year: 2012
Title: The Molecular Basis for Substrate Specificity of the Nuclear NIPP1:PP1 Holoenzyme.
Authors: O'Connell, N. / Nichols, S.R. / Heroes, E. / Beullens, M. / Bollen, M. / Peti, W. / Page, R.
History
DepositionDec 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
B: Nuclear inhibitor of protein phosphatase 1
C: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: Nuclear inhibitor of protein phosphatase 1
E: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
F: Nuclear inhibitor of protein phosphatase 1
G: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
H: Nuclear inhibitor of protein phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,51027
Polymers168,6208
Non-polymers2,89019
Water11,908661
1
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
B: Nuclear inhibitor of protein phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0718
Polymers42,1552
Non-polymers1,9166
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-33 kcal/mol
Surface area14630 Å2
MethodPISA
2
C: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: Nuclear inhibitor of protein phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5417
Polymers42,1552
Non-polymers3865
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-28 kcal/mol
Surface area14770 Å2
MethodPISA
3
E: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
F: Nuclear inhibitor of protein phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5417
Polymers42,1552
Non-polymers3865
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-30 kcal/mol
Surface area14290 Å2
MethodPISA
4
G: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
H: Nuclear inhibitor of protein phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3575
Polymers42,1552
Non-polymers2023
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-30 kcal/mol
Surface area15270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.639, 116.035, 168.093
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / PP-1A


Mass: 34941.066 Da / Num. of mol.: 4 / Fragment: PP1 binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1A, PPP1CA / Production host: Escherichia coli (E. coli)
References: UniProt: P62136, protein-serine/threonine phosphatase
#2: Protein
Nuclear inhibitor of protein phosphatase 1 / NIPP-1 / Protein phosphatase 1 regulatory inhibitor subunit 8 / Activator of RNA decay / ARD-1


Mass: 7213.829 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1R8, ARD1, NIPP1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q12972, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases

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Non-polymers , 4 types, 680 molecules

#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500 / Polyethylene glycol


Mass: 1529.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 661 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 0.08M Bis-Tris, 0.32M KF, 19% PEG1500, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.098→50 Å / Num. all: 88343 / Num. obs: 88343 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3
Reflection shellResolution: 2.1→2.14 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIX(AutoMR)model building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(AutoMR)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.098→20 Å / SU ML: 0.47 / σ(F): 0 / Phase error: 18.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1961 4261 5 %random
Rwork0.1542 ---
all0.1563 88268 --
obs0.1563 85153 96.47 %-
Solvent computationShrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.52 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.2589 Å20 Å2-0 Å2
2--1.4985 Å20 Å2
3----2.7574 Å2
Refinement stepCycle: LAST / Resolution: 2.098→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10782 0 80 661 11523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911139
X-RAY DIFFRACTIONf_angle_d1.05515130
X-RAY DIFFRACTIONf_dihedral_angle_d14.0444165
X-RAY DIFFRACTIONf_chiral_restr0.0611621
X-RAY DIFFRACTIONf_plane_restr0.0041956
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.098-2.12180.2551280.18492444X-RAY DIFFRACTION89
2.1218-2.14670.24711350.1752522X-RAY DIFFRACTION91
2.1467-2.17290.24751340.16092514X-RAY DIFFRACTION92
2.1729-2.20030.20131360.15392595X-RAY DIFFRACTION93
2.2003-2.22920.20791360.15952549X-RAY DIFFRACTION93
2.2292-2.25970.20431370.14842613X-RAY DIFFRACTION94
2.2597-2.2920.2061360.14632555X-RAY DIFFRACTION94
2.292-2.32610.21340.14862646X-RAY DIFFRACTION94
2.3261-2.36240.22731380.14942628X-RAY DIFFRACTION95
2.3624-2.40110.21771410.15332648X-RAY DIFFRACTION95
2.4011-2.44240.22791350.15232621X-RAY DIFFRACTION95
2.4424-2.48680.2121410.1532653X-RAY DIFFRACTION96
2.4868-2.53450.21541420.14872677X-RAY DIFFRACTION96
2.5345-2.58610.18151380.1512666X-RAY DIFFRACTION97
2.5861-2.64220.17681430.1542701X-RAY DIFFRACTION97
2.6422-2.70360.21611400.15712663X-RAY DIFFRACTION97
2.7036-2.7710.21621420.15932729X-RAY DIFFRACTION98
2.771-2.84570.21261460.16372754X-RAY DIFFRACTION98
2.8457-2.92920.21941400.15582698X-RAY DIFFRACTION98
2.9292-3.02340.21841470.15292758X-RAY DIFFRACTION99
3.0234-3.13110.20991470.15832752X-RAY DIFFRACTION99
3.1311-3.2560.19021460.15842774X-RAY DIFFRACTION99
3.256-3.40340.21961470.15832779X-RAY DIFFRACTION99
3.4034-3.58190.17521480.152794X-RAY DIFFRACTION100
3.5819-3.80490.19571470.15972798X-RAY DIFFRACTION99
3.8049-4.09630.17111470.14072816X-RAY DIFFRACTION99
4.0963-4.50430.14491500.11952836X-RAY DIFFRACTION100
4.5043-5.14630.16211500.12922841X-RAY DIFFRACTION99
5.1463-6.44730.21751520.17792882X-RAY DIFFRACTION100
6.4473-19.96260.17781580.19052986X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6067-0.0466-0.160.60860.27460.9602-0.0020.02160.10370.0131-0.0042-0.0068-0.1256-0.0657-0.00940.09360.0161-0.02140.06870.02350.127719.394554.138767.1193
20.0155-0.0070.0180.0594-0.05930.0995-0.013-0.0398-0.1969-0.27420.13590.2250.1375-0.0310.00350.1688-0.01760.00890.1670.02670.19198.726134.987774.4105
30.00780.003-0.0165-0.0065-0.00740.026-0.0138-0.0443-0.09560.00450.0077-0.28880.03180.02040.00010.1855-0.0254-0.01320.2328-0.00980.283115.694743.328792.0805
40.2172-0.0858-0.19680.0643-0.02511.06270.36550.17020.3225-0.03230.1979-0.1275-0.21420.09510.20590.4137-0.1167-0.09290.10120.02230.577729.846271.633467.0579
50.7103-0.19650.08191.0674-0.09080.65050.03720.1010.0143-0.0719-0.066-0.09020.02840.035-0.00640.05920.00350.00830.11240.01130.085249.978929.615863.3669
60.02260.0086-0.01790.0059-0.00230.01310.0933-0.3463-0.12350.4948-0.06530.2485-0.1601-0.0150.00010.2906-0.04750.06950.3070.04720.226135.709921.440984.2267
70.0133-0.0075-0.00140.0109-0.00290.0220.11250.1818-0.1876-0.14320.050.09830.163-0.092700.1739-0.04860.00490.2005-0.01670.28839.004811.202370.6523
80.1416-0.22530.01220.385-0.03840.01390.17660.07880.3067-0.2299-0.1709-0.4429-0.1417-0.07620.04220.2585-0.00460.11380.35180.22370.166657.536637.75346.4689
90.94490.4020.44721.62420.63081.2162-0.07370.0652-0.1472-0.04020.1551-0.1730.0483-0.01510.14870.0739-0.01670.04010.0707-0.0330.116515.6831.266161.3236
100.17870.0030.00520.0101-0.00650.0267-0.01660.12180.1640.41320.15940.0912-0.3762-0.06820.00370.4203-0.0357-0.01760.18970.0190.173910.644522.40853.4896
11-0.0003-0.0146-0.00410.23720.0520.01930.0904-0.0531-0.0168-0.07290.1839-0.24550.0694-0.1136-0.01150.50620.1042-0.02860.4293-0.050.200113.842911.606837.3319
120.37420.0310.36080.15640.07750.35570.33490.1247-0.5763-0.0630.3733-0.21670.13960.01420.40510.40350.1371-0.11480.0774-0.08020.669922.3919-18.027763.6404
131.47570.370.41491.50780.3341.43050.01920.2678-0.1246-0.25550.1091-0.15930.04630.06630.00850.2101-0.03750.00470.2248-0.04110.100816.258827.484123.0903
140.1753-0.260.13980.4176-0.17850.29520.2075-0.39610.0894-0.20530.17770.29260.1825-0.1920.1090.2536-0.15220.00590.2982-0.00470.2456-0.034418.591638.1037
150.0621-0.02580.00730.0328-0.00170.02530.05550.1011-0.0891-0.0267-0.12070.07970.1037-0.1381-0.00930.5535-0.0894-0.16220.4294-0.24570.7932-0.99017.161420.1756
160.0161-0.0151-0.02120.0180.01750.03970.01610.08840.1468-0.4772-0.0159-0.19770.21980.1343-0.00430.9819-0.18240.56510.7265-0.03860.06923.800632.72144.5245
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 7:299 )A7 - 299
2X-RAY DIFFRACTION2( CHAIN B AND RESID 160:175 )B160 - 175
3X-RAY DIFFRACTION3( CHAIN B AND RESID 176:184 )B176 - 184
4X-RAY DIFFRACTION4( CHAIN B AND RESID 199:214 )B199 - 214
5X-RAY DIFFRACTION5( CHAIN C AND RESID -1:300 )C-1 - 300
6X-RAY DIFFRACTION6( CHAIN D AND RESID -2:168 )D-2 - 168
7X-RAY DIFFRACTION7( CHAIN D AND RESID 169:177 )D169 - 177
8X-RAY DIFFRACTION8( CHAIN D AND RESID 199:214 )D199 - 214
9X-RAY DIFFRACTION9( CHAIN E AND RESID 7:299 )E7 - 299
10X-RAY DIFFRACTION10( CHAIN F AND RESID 159:175 )F159 - 175
11X-RAY DIFFRACTION11( CHAIN F AND RESID 176:182 )F176 - 182
12X-RAY DIFFRACTION12( CHAIN F AND RESID 200:214 )F200 - 214
13X-RAY DIFFRACTION13( CHAIN G AND RESID -5:298 )G-5 - 298
14X-RAY DIFFRACTION14( CHAIN H AND RESID -2:175 )H-2 - 175
15X-RAY DIFFRACTION15( CHAIN H AND RESID 176:183 )H176 - 183
16X-RAY DIFFRACTION16( CHAIN H AND RESID 198:212 )H198 - 212

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